Monday, October 11, 2010

Judge Jones: I was taken to school

In reflecting on the 2005 Kitzmiller v. Dover Area School District court case over which he presided, federal judge John Jones recalls that he “was taken to school.” Ever since his liberal arts days at Dickinson College, Jones has never doubted evolution. But his knowledge of the biological details, what little there was to begin with, was by 2005 quite stale. All that changed in the Kitzmiller case where Jones learned from various expert witnesses. It was, Jones recalled, “the equivalent of a degree in this area.” And Jones is confident his new knowledge served him well. “Folks who disagree with my opinion will tell you I never got it right,” he explains, “but I'm confident that I did.” Did he? The answer is both “yes” and “no.”

Science is a human endeavor with all the messiness that such endeavors entail. From ego battles to funding concerns, there is much that doesn’t look very much like science. But somewhere in between there is, at least sometimes, a search for truth. Hypotheses and models may be rough and approximate, but most scientists think of their work as driven by how the world really works.

Law is a very different endeavor. One of the basic tenets law students learn is to apply the law. That is not always as obvious as it may seem. Both the law and the evidence may be complicated, and the application may violate your knowledge or even common sense. So be it, that is how our legal system works.

In fact judge Jones did not research evolution or Intelligent Design for the Kitzmiller case. The law is applied to the evidence, and the evidence is provided in the court case itself. Jones understood the law and its application, but the evidence would be given to him. As Jones recalls:

The very first witness for the plaintiffs was Ken Miller. He is very invested in this issue. He writes a textbook that is used substantially in high school biology classes throughout the country. And I think it's fair to say that the plaintiffs knew what they had in terms of their judge. They knew that I was not a scientist, but hopefully that I had a reasonably good head on my shoulders, that they were going to need to take me to school. So their first witness did just that.

Yes Miller did take Jones to school. Jones was heavily influenced by Miller’s testimony which contained several compelling evidences for the fact of evolution. Unfortunately those evidences were not true.

Before the trial Miller and the ACLU lawyers had carefully designed Miller’s testimony to persuade the Dover court lay audience that Darwin’s idea was scientific and absolutely undeniable—a no-brainer.

But to do so they would need to twist the truth. Ever so slightly they manipulated the scientific evidence. And in science, subtle adjustments can make all the difference. Here are some of the lies that Miller fed to Jones.

Lie #1 A pseudogene has no function and is broken

Miller’s first powerful evidence for evolution came from pseudogenes, DNA sequences that are similar to genes but have important differences. Miller’s example was the beta globin pseudogene which he described as non-functional and broken:

2 If you could advance the slide, please.
3 I've zeroed in on the six copies of the beta-globin
4 gene sequence. Each of these copies is a set of
5 instructions for how you build this polypeptide. Five
6 of them work, but one of them doesn't. It's given the
7 Greek letters psi, beta, and then the number one. And
8 the psi-beta-1 sequence isn't a gene. It doesn't
9 work. It's a pseudogene, and a pseudogene is
10 recognized as a gene because it's so similar to the
11 other five in its DNA sequence, but it has some
12 mistakes. It's broken, and it has a series of
13 molecular errors that render the gene non-functional. [79]

The lie here is not in the word “broken” but in the word “is.” It is reasonable to think that the beta globin pseudogene is broken, but we don’t know this for certain. I suspect it is, but we can’t say with certainty that it is broken. In fact we still have much to learn about the biomolecular world.

Whether the pseudogene is simply broken or has some subtle, perhaps rarely used, function is difficult to say. My guess is the former, but to be sure the history of evolutionary thought is full of such claims gone wrong. From the appendix to the thyroid gland, evolutionists have been quick to claim non function for structures that years later are found to do various jobs. And this holds even for some pseudogenes.

And while a consistent function has not been found for pseudogenes in general, it is difficult to be sure that the beta globin pseudogene, for example, is non-functional and broken, as Miller unequivocally informed the court. The distinction may seem to be minor, but it was crucial to Miller’s case.

Lie #2 Pseudogene DNA sequences have “errors” or “mistakes”

While informing the court that the beta globin pseudogene is broken, Miller also explained that its DNA sequence has “errors” or “mistakes.”

14 Now, I'd like to show you exactly what those
15 molecular errors are in the next slide. This is a
16 blow-up of the pseudogene. These are the portions
17 that actually do the coding, if it was coded in red
18 here. And you'll notice that there are six distinct
19 mistakes in this gene.
20 Now, I don't know if I really want to try
21 the patience of the Court in terms of going into the
22 details of molecular biology, but in a very simple
23 way, the altered initiator means that the signal that
24 exists at the front of the gene that says "copy me" is
25 missing. And therefore RNA preliminaries, the
1 molecule that copies genes, can't bind, and it never
2 gets expressed.
3 But even if it did get expressed, it has
4 five other errors that would keep this, the RNA copy
5 of this gene, from being translated. It's missing the
6 start signal. It's got stop codons that would cause
7 the synthetic apparatus to grind to a halt. It's just
8 a mess. [79-80]

Just as we are not certain that the pseudogene has no function and is broken, likewise we are not certain that its DNA sequence contains “errors” or “mistakes,” caused by mutations. That certainly could be the case, but it may not be.

As we will see shortly, Miller will use this claim as circumstantial evidence for evolution. What Miller did not inform the court of is that globin genes (from which the pseudogene is supposed to derive) have about 140 amino acid residues, and since there are 20 different amino acids this means there are 20^140 sequences for evolution to choose from in creating a globin gene. This number, 20^140, is astronomically huge. It is equivalent to a 1 with more than 180 zeros after it.

And of all those different sequences, only a tiny fraction result in a functioning globin protein, meaning that it is highly unlikely evolution could have luckily hit upon the globin design in the first place. This is to say nothing of how the molecular machinery to construct the protein, and make use of it once constructed, could have already been in place.

Furthermore, there are a great many proteins that are far bigger, and so even less likely to have evolved, than the globin protein. Evolutionists have little more than just-so stories to explain how such genes arose, but judge Jones’ new biology degree did not include such conundrums.

Lie #3 There is no reason for broken genes aside from common descent

Miller next move was to evolution’s venerable “shared-error” argument that has swayed so many. If these DNA errors or mistakes are found to be repeated in different species, then those species must have evolved via a common ancestor.

9 Now, the reason that this is important in
10 evolution is actually very simple, and that is, these
11 errors appear in a gene, they have no functional
12 purpose. And you might ask yourself, what would I do,
13 what would you do if we were to find another organism
14 that didn't just have similar genes but also had a
15 pseudogene in the same spot and had the same set of
16 errors?
17 There's no reason why evolution would
18 produce a duplicate set of mistakes in two copies of
19 things. It must mean that these two organisms are
20 descended with modification from another organism that
21 had the same set of mistakes.
22 And if you go on to the next slide, what I'd
23 like to show you are three organisms, the gorilla, the
24 chimpanzee, and the human being that share the exact
25 same set of molecular mistakes.
1 Now, why is this significant? One of the
2 core principles of evolution is common descent. One
3 could always argue that because the three species that
4 I've depicted on this slide are all African species,
5 that's where they all come from, they're all primates
6 and they all probably started out living in similar
7 environments, that the functional parts of this gene
8 locus, they might work the same. But you cannot argue
9 that the mistakes should match.
10 And the fact that all three of these species
11 have matching mistakes leads us to just one
12 conclusion, and that's the same conclusion that
13 Charles Darwin predicted almost a century and a half
14 ago, and that is that these three species share a
15 common ancestor. Matching mistakes are evidence of
16 common ancestry. [80-81]

But as any expert witness would know, this is not true. Assuming that the beta globin pseudogene is indeed broken, and that the DNA sequence “errors” are indeed errors, there is no reason to conclude they must have arisen via a common ancestor. Even evolutionists agree with this obvious fact.

Shared errors can arise from the independent occurrence of like mutations. Indeed, from viruses and bacteria to primates, like mutations that must have occurred independently (even if evolution is true) have been repeatedly observed. Similarly, mutational “hotspots” are common and, of relevance here, have been observed in pseudogenes.

In fact, comparison of pseudogenes in different species have forced evolutionists to conclude that like mutations must occur independently. Urate oxidase pseudogenes are just one such example, and it simply is false that such similarities can only be explained by common descent.

Lie #4 This is objective science

Even if there were no examples of independent, shared mutations such as in the urate oxidase pseudogenes, Miller’s argument is not objective science as he presents it to be. Miller gave testimony about how science works, but here uses the shared-error argument which is a metaphysical argument that goes back centuries.

Miller informed the court that these shared errors “must mean that these two organisms are descended with modification from another organism” and “the fact that all three of these species have matching mistakes leads us to just one conclusion, … that is that these three species share a common ancestor.”

But how does Miller know that common descent is the only possible explanation? As I have discussed before, this is one of the many entry points of evolutionary metaphysics into science. Evolutionists consistently make this claim that only their theory can explain what we find in biology, and such a claim requires knowledge unavailable to science.

The short explanation is that this shared-error argument is a form of an IF-AND-ONLY-IF statement, which is non scientific. The long explanation is that the non scientific element arises from Enlightenment theology, supplied by Lutherans and Roman Catholics on the continent and Anglicans in England in the 17th and 18th centuries. It entered into science mainly via evolutionary thought. Darwin repeatedly used the argument and it is now rampant in the evolutionary apologetics literature. As Stephen Jay Gould explained:

Odd arrangements and funny solutions are the proof of evolution--paths that a sensible God would never tread but that a natural process, constrained by history, follows perforce. No one understood this better than Darwin. Ernst Mayr has shown how Darwin, in defending evolution, consistently turned to organic parts and geographic distributions that make the least sense.

Elliot Sober, a philosopher who analyzes evolutionary arguments in great detail has explained how the argument works in terms of likelihood ratios. Sober refers to the argument as Darwin's Principle. As he explains,

Adaptive similarities provide almost no evidence for common ancestry while similarities that are useless or deleterious provide strong evidence for common ancestry.

Miller’s “broken” pseudogenes with their DNA “errors” were the perfect example of such useless similarities. And why are useless or deleterious similarities so helpful? It is not because they raise the probability of common ancestry, but rather because they lower the probability of separate ancestry. In other words, the reason common descent is a no-brainer is that the alternative, separate creation or design, is extremely unlikely.

From before Darwin to Miller this argument has been a crucial weapon in evolution’s apologetic arsenal. Miller began using this non scientific argument against Intelligent Design when the new movement first began. He was well practiced by the time the Kitzmiller opportunity arose, and the small-town Lutheran lawyer from Pennsylvania coal country didn’t stand a chance. Did judge Jones “get it right” as he so confidently asserts? Yes, he correctly applied the law, but he applied it to a set of lies.

92 comments:

The lie here is not in the word “broken” but in the word “is.” It is reasonable to think that the beta globin pseudogene is broken, but we don’t know this for certain.

We don’t know anything for certain in science (or in ordinary life), but when the weight of evidence is great, we can with straight faces declare something a fact. In court, a judgment must be made “beyond a reasonable doubt,” which means without certainty.

Lie #2 Pseudogene DNA sequences have “errors” or “mistakes”

Just as we are not certain that the pseudogene has no function and is broken, likewise we are not certain that its DNA sequence contains “errors” or “mistakes,” caused by mutations. That certainly could be the case, but it may not be.

What I said in response to #2 also applies here.

Lie #3 There is no reason for broken genes aside from common descent

But as any expert witness would know, this is not true. Assuming that the beta globin pseudogene is indeed broken, and that the DNA sequence “errors” are indeed errors, there is no reason to conclude they must have arisen via a common ancestor.

Cornelius, your arguments, if true, would also apply against paternity testing, DNA fingerprinting, etc. It's precisely the same concept -- shared genetic similarity is evidence of genetic relationship. Courts accept it routinely in the forensic situation -- where people's lives are literally on the line! -- yet it magically becomes "lies" all of the sudden when used in support of evolution.

You wonder why creationists keep on losing in court? Your post is an example of why. You couldn't critically examine your own argument or provide a balanced assessment of it if you tried. Which you don't. You have no sense of the weak spots, or the damage your arguments would do to vast areas of science, law, etc., which even you accept, if applied consistently...

"In other words, the reason common descent is a no-brainer is that the alternative, separate creation or design, is extremely unlikely."

In Fisherian statistical testing, the reason the alternative hypothesis is a no-brainer is that the alternative, the null hypothesis, is extremely unlikely (P<0.05, or less than a 5% probability that the observed results occurred by chance). This is the exact same logic applied above. So are all these statistical tests applied in all areas of basic and applied science lies as well?

A lie, Cornelius, is a deliberate misrepresentation of fact. By accusing Ken Miller of lying about pseudogenes, you are suggesting that he knew that pseudogenes actually work but chose to tell the judge otherwise.

This is just preposterous. If Miller were indeed lying, surely the experts testifying for the defendants could point that out to the defense attorneys and they would pin him during the cross examination. That did not happen. Why not? I can suggest three reasons. (i) The defense experts were incompetent. (ii) The defense attorneys were incompetent. (iii) Miller's statements weren't lies.

Much as I am sympathetic to Reason (i), I would have to go with (iii). Science is not a search for the Truth with a capital T. Its conclusions are tentative and can be overturned in the future. We do not know for sure that gravity works the same way on the scale of the solar system but we have pretty good observational evidence that it does: the outer planets of the solar system move in accordance with Kepler's laws. Maybe there is no gravity beyond the orbit of Mars and maybe angels do keep the outer planets in orbits, but to suggest that the law of gravity is a lie is balderdash.

Likewise with pseudogenes. We do not know for certain that every single pseudogene arose as a result of a copying error, but the mechanics of such errors is well understood and the evidence is sufficiently strong that it is considered noncontroversial by scientists. That was enough for the court.

You can speculate all day long that pseudogenes aren't errors but are deliberate work of an intelligent designer, but speculations aren't convincing arguments. You need evidence for that and you don't have any. The only option left to you is to accuse the other side of lying. Do that often enough and you will lose credibility. In fact, I think you have already lost it. I wonder if anyone outside creationist circles considers you seriously. I bet not.

Yes, Hunter's accusations of lying are bombastic. A softer word on his part would turn away wrath like yours. But he's not talking to you; he's talking to the Creationist crowd, which doesn't do nuance.

Cornelius Hunter: Assuming that the beta globin pseudogene is indeed broken, and that the DNA sequence “errors” are indeed errors, there is no reason to conclude they must have arisen via a common ancestor.

It's not a random distribution of errors, but a nested hierarchy. Furthermore, globins form a family of proteins!

Cornelius Hunter: And of all those different sequences, only a tiny fraction result in a functioning globin protein, meaning that it is highly unlikely evolution could have luckily hit upon the globin design in the first place.

If Miller's arguments were so weak, then what does that say about the other side. They must have been incompetent not to have picked up on these errors and exposed them to the court. That is what the court process is designed to do. They had an opportunity to expose these errors but failed. Perhaps Judge Jones was a good choice as a judge because he had little background in the case. .

What Miller did not inform the court of is that globin genes (from which the pseudogene is supposed to derive) have about 140 amino acid residues, and since there are 20 different amino acids this means there are 20^140 sequences for evolution to choose from in creating a globin gene. This number, 20^140, is astronomically huge. It is equivalent to a 1 with more than 180 zeros after it.

And of all those different sequences, only a tiny fraction result in a functioning globin protein, meaning that it is highly unlikely evolution could have luckily hit upon the globin design in the first place.

If you don't want Intelligent Design to be conflated with creationism, you should stop using discredited creationist arguments to support ID.

This is nothing more than the old "tornado in a junkyard" claim, complete with big numbers to impress the credulous. No one with even a minimal understanding of biology would suggest that the proteins you're discussing arose de novo. If you don't know better, you shouldn't be posting on the topic. If you do know better, you should stop being so dishonest.

In fact, comparison of pseudogenes in different species have forced evolutionists to conclude that like mutations must occur independently. Urate oxidase pseudogenes are just one such example, and it simply is false that such similarities can only be explained by common descent.

Whenever I read of Dr Miller's junk dna and pseudogenes non-function I can't help but think of a man that is not interested in leaving a good legacy.

He's constantly writing about junk this and junk that and even while the ink on his articles has hardly had a chance to dry, others are finding that the so-called junk DNA has purpose.

Also, here's a link on a possible purpose of pseudogenes... http://www.sciencenews.org/view/generic/id/60515/title/Vestigial_no_more

Darwinists are so quick to jump on the junk-dna bandwagon. Does their theory slow down research into dna and gene function??? Since it's junk, then why look for a purpose?

That's a good question. Obviously a number of scientists continue to investigate "junk"-dna and pseudogene function.

With the prediction record of evolutionary theory being as poor as it is, it would be wise to invest in research that seeks to disprove the prediction. The odds are real good at finding more use for the so-called "junk" dna and pseudogenes.

I'm sure that whenever function for junk dna or pseudo-genes is found that evolutionary theory will be falsified. No? Interesting.

In this case it was because A) the school board was religiously motivated and didn't know what ID was and B) Jonesy didn't listen to the ID experts- rather he took the word of the anti-IDists on an agenda against the words of the real experts.

However if this happens in my district- which I predict it will- the anti-ID side won't get away with their lies as I will be right there pointing them out.

Darwinists are so quick to jump on the junk-dna bandwagon. Does their theory slow down research into dna and gene function??? Since it's junk, then why look for a purpose?

The term 'junk DNA' is one used by the popular press. The proper scientific term is non-coding DNA. ToE doesn't say that there will be no use for such DNA, it merely says as of now most of it has no known use.

If you have to stick with the popular press term, understand that 'junk' doesn't mean useless. It's more like the 'junk' drawer everyone keeps in their kitchen It ends up being filled with all sorts of still good but currently not used pieces of miscellaneous hardware - screws, washers, rubber bands, the third AAA battery in the pack when you only needed two, etc. And just like evolution, you never know when some small article from the drawer might be just the thing to do some important household repair.

What Miller did not inform the court of is that globin genes (from which the pseudogene is supposed to derive) have about 140 amino acid residues, and since there are 20 different amino acids this means there are 20^140 sequences for evolution to choose from in creating a globin gene. This number, 20^140, is astronomically huge. It is equivalent to a 1 with more than 180 zeros after it.

And of all those different sequences, only a tiny fraction result in a functioning globin protein, meaning that it is highly unlikely evolution could have luckily hit upon the globin design in the first place.

That's really pathetic CH, even for you. Do you not understand high school level probability theory either? The probability would be 1 in 20^140 for that protein only if the protein had to self assemble from its constituent parts all at once. But evolution doesn't work like that. It's a long term iterative process where each generation accumulates and builds on the successes of the previous generation.

You can't calculate the probability of an iterative feedback process by taking a one-time snapshot and multiplying individual probabilities. You have to know the history and the rules of the process at each stage to get any meaningful numbers.

Creationists make a lot of incredibly stupid logic errors, but the "argument from heap big numbers" ranks right at the top of the list.

I think you're reading into Miller's testimony something that he doesn't say (and that Darwin, Wiedersheim, etc. also didn't say): that vestigial organs have no function whatsoever. Darwin (who referred only to organs, and called them "rudimentary," not "vestigial") nonetheless set the pattern when he noted that a structure could lose its most conspicuous function and still remain useful for other functions. Indeed, from a "Darwinist" perspective (as Wiedersheim pointed out), it could be coopted for functions it had not performed in the ancestral state.

Anyway, whether the beta-globin gene is "broken" is determined not by whether it serves some biological function, but by whether it serves the biological function of making beta-globin, as its homologues do. Other functions leave unexplained why it should so closely resemble a beta-globin gene.

And yes, coincidences happen. It's asking rather more of coincidence (it is, as they say, "less parsimonious") to infer that (if we're talking about what evolution would do) mutations and natural selection shaped something that looked so much like a beta-globin gene even though it didn't perform the most conspicuous function of a beta-globin gene (which, again, is making beta-globin) than to suppose that such mutations copied and disabled an already-existing gene that did indeed originally code for beta-globin.

And at the risk of being "theological," it seems the same argument applies to a Designer. Never mind assumptions about the Designer's design philosophy or methods (unless the assumption is that the Designer is deliberately trying to trick us into thinking we're the products of evolution): what are the odds that the Designer would see a point to making something that looked like a disabled beta-globin gene but had some completely different function, compared to the odds that a beta-globin gene existed once at that locus but was disabled by mutation?

Such accounts of the trial as I've read suggest that the judge did listen to them. This may have been part of their problem: when, e.g. Behe acknowledged that the sheer volume of relevant papers he had not considered when making the claims he did in Darwin's Black Box, it could not have helped his claims.

Granted, this may have had less to do with the specific outcome of the case than, e.g. Bill Buckinham repeatedly perjuring himself on the stand about his conduct on the school board, or his and other board members' palpable cluelessness about how either evolution or ID were supposed to work. But Behe's response to cross-examination could not have helped the case.

Then, of course, there were the ID experts who refused to testify: Bill Dembski famously refused to present his case in court.

Also the judge refused to allow the publisher of the book to be represented.

The book publisher wasn't being sued. What was he going to testify to: that the previous editions of the book discussed in the trial did not, in fact, really exist? That the infamous "cdesignproponentists" "transitional form" in one draft did not exist?

IOW it was rigged.

Why evos think that a rigged trial helps them make their case is beyond me.

Reality demonstrates an anti-creationist bias. Any trial that deals with reality is likely to be "rigged" against cdesignproponentists.

Junk DNA was not an invention of the popular press and media but it came from Dr. Susumu Ohno, writing in the Brookhaven Symposium on Biology in 1972 in the article "So Much ‘Junk DNA' in our Genome".

Funny how evolutionists are constantly trying to put a happy face on obvious predictions gone bad. If their not in denial then they'll play shell games with word definitions.

"We didn't mean "Junk", as in "Junk"... its the media's fault, etc, etc."

Here's a prediction from design viewpoint: The known levels of regulation and control within the genome will continue to grow as research expands, more functions will be found for Junk-DNA and pseudogenes, some of them being critical to the genome, and the systems integration found within the genome will become staggeringly complex. It will be akin to the number of scientists who truly understand the math of the theory of general relativity. Evolutionary theory will run in denial of its old stance about junk dna and pseudogenes and stagger under the weight of new shell games and hypotheses to plug the increasing number of holes in its framework.

Neal Tedford: Junk DNA was not an invention of the popular press and media but it came from Dr. Susumu Ohno, writing in the Brookhaven Symposium on Biology in 1972 in the article "So Much ‘Junk DNA' in our Genome".

So evolutionary theory was invented by Ohno in 1972?

A simple view of evolution is that it will tend to remove unneeded structures over time. But small, slow reproducing organisms can accumulate and sustain more junk. There are countervailing influences.

Neal Tedford: Here's a prediction from design viewpoint: The known levels of regulation and control within the genome will continue to grow as research expands ...

That's not much of a prediction. As most of the genome is still a mystery, all you are predicting is that as we explore more of the genome, we will learn more about the genome.

CH, Yes Miller did take Jones to school. Jones was heavily influenced by Miller’s testimony which contained several compelling evidences for the fact of evolution. Unfortunately those evidences were not true.

Pity Craig Mello didn't know you CH. Or else he would have disregarded what Miller taught him at Brown, given up his futile studies in biology and gone on to achieve loftier things.

JoeG,Whining = [world's tiniest violin+"they cheated"+case you soundly lost five years back]

It was a sorry day for science when Dr Miller can dismiss Irreducible Complexity by wearing a mouse trap for a tie clip and mention that type III secretion system is a component of flagella.

It's like saying that a lug nut is a component of an engine therefore an engine is not irreducibly complex. Judge Jones either did not understand irreducible complexity or he willfully dismissed anything that didn't jive with what Ken Miller said.

Thank you for the excuse to revisit the Dover case which I found fascinating.

First, as to FTE's late request to directly participate in the Dover Trial. It was laughably disengenuous of them to claim they were unaware the trial was about ID versus Evolution in general and their book specifically until all the depositions were just about completed.

Both the Plantiffs' and the Defendants' lawyers requested that the judge deny the last minute request.

From the Judge Jones' motionhttp://www.pamd.uscourts.gov/kitzmiller/04cv2688-111.pdf

"First, at this late date, the Court would have expected a coherent statement of what FTE intends to prove or demonstrate if the Court were to permit intervention, as well as specific reasons as to why the Defendants are not adequately protecting FTE’s interests; however, despite repeated questioning in that regard by the Court during the July 14, 2005 hearing, FTE was unable to verbalize how its interests and the Defendants’ interests diverge concerning the merits of the lawsuit. Moreover, Buell’s testimony revealed that the very experts that insisted on private counsel from FTE to provide confidential legal advice in preparation for and during expert depositions, Dembski and John Campbell (“Campbell”), which resulted in their being terminated as experts for Defendants, will be brought back into this case if FTE is permitted to intervene. It is absurd to the Court that Buell has now testified on multiple occasions that he would go to jail prior to revealing the draft text of The Design of Life; however, if the Court allows FTE to intervene, Buell would place that issue squarely back into play by FTE’s apparent intention to use Dembski as its expert witness."

As to Of Pandas and People being about creationism, starting on page 99...

"Intelligent design means that various forms of life began abruptly through an intelligent agency, with their distinctive features already intact - fish with fins and scales, birds with feathers, beaks, and wings, etc."

In the draft version it was...

"Creation means that the various forms of life began abruptly through the agency of an intelligent creator with their distinctive features already intact. Fish with fins and scales, birds with feathers, beaks, and wings, etc."

IMO, Judge Jones handled the situaiton extremely fair to both side and clearly ruled correctly considering the evidence presented in the courtroom.

Joe wrote: Why evos think that a rigged trial helps them make their case is beyond me.

Rigged?

Dembski, Meyer and John Campbell from the Discovery Institute were previously scheduled witnesses in the case, but they backed out before the trial began. Ends up Bruce Chapman, director of the Discovery Institute asked them not to testify, along with Behe and Minnich, who testified anyway.

I have several items that either no longer work and/or are not used for their original purpose. which I keep for sentimental reasons. However, I would not be offended should someone call them junk. This is because I understand how the term junk is defined and that these items actually fit that definition.

Yes, despite the fact that clarifications have been presented time and time again that the term Junk DNA does not imply universal non-function, we continue to see the same mischaracterization trotted out over and over again by ID proponents.

So, it would seem that the real issue here is that ID finds the terms used by evolutionary theory offensive.

As much as I disagree with him on probably just about everything ;-) I do have to give Cornelius a compliment: your moderation policy puts many other sites to shame. I mean, I can´t imagine some of comments people write here don´t hit a nerve sometimes. Yet you keep churning out your posts, and the open discussion continues. Respect!

Mark said: 'As much as I disagree with him on probably just about everything ;-) I do have to give Cornelius a compliment: your moderation policy puts many other sites to shame. I mean, I can´t imagine some of comments people write here don´t hit a nerve sometimes. Yet you keep churning out your posts, and the open discussion continues. Respect! '

"Junk" as in junk-dna was coined, not by the media, but by a scientist. The "junk-drawer" spin on the definition of "junk" seems to be gaining traction among evolutionists who are creatively trying to distance themselves from the more disparaging use of the term as it was originally coined. However, even there they shall find no hiding place.

Rather than biological junk drawer items, they are looking to play a fundamental role in life itself:

http://www.nature.com/news/2004/040503/full/news040503-9.html

"If you thought we had explored all the important parts of our genome, think again. Scientists are puzzling over a collection of mystery DNA segments that seem to be essential to the survival of virtually all vertebrates. But their function is completely unknown.

The segments, dubbed 'ultraconserved elements', lie in the large parts of the genome that do not code for any protein. Their presence adds to growing evidence that the importance of these areas, often dismissed as junk DNA, could be much more fundamental than anyone suspected..."

The whole "junk-dna" concept was a direct implication and prediction of evolutionary theory. They jumped the gun before all the facts were in (like Tiktaalik) based on the predictive power of evolutionary theory.

It is another example of evolutionary theory misleading the way forward.

Growing up towards the end of the cold-war I sometimes listened on shortwave to Radio Moscow during the waning days of the former Soviet Union. Their Pravda broadcasts were 100% Darwinist and atheist, always putting a good spin on the communist government. Their bias against the West and Creationism was evident in their broadcasts.

The USSR would "jam" western broadcasts from being heard over shortwave.

The USSR was the biggest experiment in atheism and practical Darwinism in history over a period of 70 years. Atheists claim that the problems of the world are caused by religion. Well we've seen what happens when atheism is in charge. Millions sent to Siberia, mental institutions, and prisons. Millions tortured and killed. Finally, economic collapse.

Yet, the Berlin wall did come down and the USSR is now known as the "former" USSR.

It should give all those who believe that life was designed... hope that even the hardest and strongest of supporters of Darwinism will one day leave their ideology and embrace the evidence. Truth ultimately prevails.

Why don't you write a letter to all the thousands of genetic researchers whose work is published Nature, Science, PNAS, Cell, Journal of Evolutionary Biology, etc. and tell them they're doing Satan's work by misleading the way forward?

Better yet, why don't you tell us now how all those researchers should be doing their work differently. Seems to me they've been pretty successful so far. What do you have to offer that's better, and why haven't any Creationist researchers actually tried it?

Growing up towards the end of the cold-war I sometimes listened on shortwave to Radio Moscow during the waning days of the former Soviet Union. Their Pravda broadcasts were 100% Darwinist and atheist, always putting a good spin on the communist government. Their bias against the West and Creationism was evident in their broadcasts.

Gee Tedford, I remember hearing Christian evangelists on the radio like Jim Bakker, Jimmy Swaggert, Ted Haggard, Kent Hovind, George Alan Rekers, etc. and other shining examples of Christianity. Based on their behavior should I conclude all Christians are liars, cheats, and gay sex addicts?

The broadcasts by Radio Moscow to their overseas listeners that I listened were back in the 1970's. It is too far back to remember specific broadcasts, but the Marxist and Darwinist themes were hyped as better than capitalist and religious based societies. The ideology stuff was very evident in their broadcasts. It was kind of like the NY Times now, where they run articles about evolution from time to time.

I'm wondering if teachers in Russia today have more liberty to teach ID than their American counterparts.

People are fallible and some fail in any endeavor. That's not what I'm talking about. The USSR was, as President Reagan said, an evil empire. It was a whole system based on marxist and atheist ideology to the point of forcing a good chunk of the world to conform. Are you comparing the failures of some Christian evangelists to the atrocities of the USSR? I don't recall any of them sending people to hard labor or death in Siberia, do you?

People are fallible and some fail in any endeavor. That's not what I'm talking about. The USSR was, as President Reagan said, an evil empire. It was a whole system based on marxist and atheist ideology to the point of forcing a good chunk of the world to conform. Are you comparing the failures of some Christian evangelists to the atrocities of the USSR? I don't recall any of them sending people to hard labor or death in Siberia, do you?

You're the idiot who tried trying USSR political events to the veracity of evolutionary biology.

If political events in the USSR somehow discredit ToE, then the behavior of Christian evangelists discredits all of Christianity.

Thorton implied that it was irrational to use the term "junk DNA." However, it was Ohno who coined the term in 1972. (http://www.junkdna.com/)

No matter which term is used, the early belief was that non-coding DNA was meaningless refuse left over from earlier ancestors. Hence, studying non-coding DNA was considered to be a waste of time.

Hence, the big surprise when, increasingly, non-coding DNA was found to have function. This violated one of the supporting hypotheses of Common Ancestry. Non-coding DNA was thought to provide some support for Common Ancestry, but this support evaporated as more and more function was found for non-coding DNA.

I am well aware of the anti-religious internal policies in the Soviet Union. Churches were converted into warehouses and participation even in the officially sanctioned, Orthodox Christian Church, was frowned upon.

But I find it unlikely that the external propaganda had a strong anti-religious component. I may be wrong on that.

But that's just a side show. I am still waiting for you to back up your assertion that Radio Moscow had anything to say on the subject of evolutionary biology. It wasn't part of the internal government propaganda and I strongly doubt that it was on the agenda of Radio Moscow.

I'm still waiting for a creationist to explain to me how finding functionality in some "junk" DNA falsifies evolution. Even the coiner of the phrase, Ohno, was hypothesizing functionality from the beginning.

And SOME functionality is the key word. Vast stretches of many genomes are mobile element cemeteries. Huge sections can be deleted without ill effect:

Rather than biological junk drawer items, they are looking to play a fundamental role in life itself:

Neil,

Given that these discoveries were made by scientists, I fail to see your point.

As such, it seems you're displaying your ignorance regarding what the term Junk DNA really refers to from a scientific perspective, or your merely offended by the term.

Do you have a problem with using the term 'atom' to describe the base unit of a chemical element? Because atom, comes from the Greek - atomos 'indivisible' - yet we know atoms can indeed be split.

Just as atom only means indivisible in regards to chemical elements, Junk DNA only means junk in respect to coding for proteins. This could refer to genes that coded for specific proteins in earlier species or may have never coded. However, this does not imply universal non-function.

For example, old Macintosh computers that are turned into fish bowls technically meet the definition of the term junk as they are no longer used as computers.

www.theapplecollection.com/Collection/MacAquarium/index.shtml

Furthermore, the continued use of the term 'atom' hasn't stopped us from exploring the quantum world, including spending billions of dollars on high-energy particle research facilities, such as the LHC.

Given that clarifications have been presented time and time again that the term Junk DNA does not imply universal non-function and you've quoted a paper from scientists who are actually researching Junk DNA, it appears that you merely find the term offensive for reasons which are obvious.

The USSR was the biggest experiment in atheism and practical Darwinism in history over a period of 70 years. Atheists claim that the problems of the world are caused by religion. Well we've seen what happens when atheism is in charge. Millions sent to Siberia, mental institutions, and prisons. Millions tortured and killed. Finally, economic collapse.

An even bigger atheist experiment - Communist China - is cleaning our clock, and very successfully - is a spectacular success. It is pretty obvious you don't read the news, no I don't mean the mush that passes off for news on your favourite local network. The power of the former USSR is now wielded by the Russian Federation. The federation continues to be a scientific heavyweight (as always) is sitting on vast treasure of natural resources, is seeing the first stirrings of a population spike, and scientists returning in droves to Moscow and Sankt Peterburg. The republics that broke away have realigned with Russia - Ukraine and Georgia where we tried to set up fifth columns have since turned away from us. Bric - Brazil, Russia, India, China are surging ahead thanks to a stern adherence to the ways of science. Creationists and climate denialists are kept for amusement (not elected to public office like we allow). Crank economics of the Miltonian variety is treated like a museum piece (Keynesianism rules big time in the Bric)

In the meanwhile we in the US pick cranks and quacks like Kookinelli in Virginia to harass scientists.

Neal you should watch late night shows from Europe and Brazil. They make fun of our pseudoscientists and our anachronistic politics. And nothing but immense respect for our scientists and universities. The 2009 Chemistry Nobelist Venky Ramakrishnan, on his his first visit to India was all praise for the Indian bureaucrat and politician for their scientific understanding, unlike some cities and states in the US where millions of taxpayer money is blown up on quackery like ID-Creationism.

jbeck wrote: The power of the former USSR is now wielded by the Russian Federation. The federation continues to be a scientific heavyweight (as always) is sitting on vast treasure of natural resources, is seeing the first stirrings of a population spike, and scientists returning in droves to Moscow and Sankt Peterburg.

You've got to be kidding. Here is a recent (2007) assessment of the state of Russian science from one of the top Russian physicists who stayed in Moscow and heads the Landau Institute for Theoretical Physics.

Despite 15 years of turbulent change, 'brain drain' and a shortage of research funds, Russian science has survived, although in a much diminished state. International investment and collaboration over the next ten years could bring it back from the brink.

A few specifics:

a few of the best Russian research groups, which are internationally competitive in experimental condensed-matter physics (the field I am familiar with), have a current research budget that amounts to 3–5% of those of their similarly sized counterparts in the USA. In the long run, it is not sufficient money to compete, any amount of enthusiasm notwithstanding. The same groups could be fully functional with about 20% of the typical level of American funding. Now that Russia is literally flooded with oil and gas money, do we have any chance of getting that level of funding?

Zach: "A simple view of evolution is that it will tend to remove unneeded structures over time. But small, slow reproducing organisms can accumulate and sustain more junk. There are countervailing influences."

The trains run faster in China too. They are turning towards much more of a capitialistic economy and reaping benefits especially from unfair trade practices with a very wealthy America. So that's it ibeck? Millions still live grave poverty, they lack freedom of worship and political freedom and the freedom of speech.... but they have a booming economy and they have nice military parades. It's the atheistic utopia of the 21st century, because the economy is all that matters. Is that it?

America has been the pioneer of science since Ben Franklin. We think out of the box. Lining up to an ideology like Darwinism because the elite tell us we have to still ticks us off. Settle the debate by actually providing evidence of macro-evolution. All you have is a weak hypothesis.

I think your last sentence about millions in taxpayer money blown on ID is totally ungrounded. Are you kidding? It is the evolutionary research programs that feed from the government funding. Are you just throwing all this nonsense out to antagonize or do you really believe it?

TomH said: "Hence, the big surprise when, increasingly, non-coding DNA was found to have function."

Tom, who do you think it was that found said function?A group of pastors with a gene sequencer in the parsonage? A creationist of any sort? NO. Scientists are the ones contributing to the understanding of the genome. All the creationists do is whine and complain. They never do any original research themselves.

If you thought we had explored all the important parts of our genome, think again. Scientists are puzzling over a collection of mystery DNA segments that seem to be essential to the survival of virtually all vertebrates. But their function is completely unknown.

Neil,

Do you have any experience solving problems? I'm asking because it appears that you've mistaken known problem solving techniques for a conspiracy theory.

For example, I had a friend who's clutch in his car started getting weak and eventually went to the floor without any resistance. Since he wanted to drive his car, the problem solve was how to return the entire clutch system to normal operation.

What is the most efficient way to go about doing this?

There are several sub-systems that could cause the entry clutch system to stop working. However, the tests required for each subsystem varies significantly in complexity and effort. So, we perform the most simple tests and procedures first. In this case, this meant checking the hydraulic fluid level above the master cylinder, cracking the bleeder nipple on the slave cylinder and looking for fluid when the clutch is pumped, etc.

Just because I first check the fluid level, then check for pressure from the master cylinder, etc., this doesn't mean I've ruled out the slave cylinder as the failed sub-system. Replacing he slave cylinder might be necessary, but I want to rule other sub-systems first because replacing it takes significantly more time and the procedure is much more complex.

So, given the goal to return the entire clutch system to operation, there is a specific best-practice approach to reaching that goal.

We can say the same thing regarding understudying biological complexity.

One of our goals is to understand how our genome translates into specific features. Studying coding DNA first does not mean that non-coding DNA might have some extremely complex influence on expression. It simply represents good problem solving skills.

Now, if the problem you're trying to solve how to get science to accept your particular theological beliefs on origins, rather than say, cure cancer, alzheimer's or birth defects, then yes. You might consider looking everyone at once might be the most efficient path.

The problem with evolutionists is that they jumped on the junk dna bandwagon and talked about how it was predicted that evolution expected a lot of useless leftovers in the genome.

They created the monster you are attempting to make excuses for!

We would not be having this discussion had they simply held off on the evolutionary judgments and said, "there are regions of the genome that are non-coding but we are investigating their function further". Period. No, they used the non-coding region to promote their prediction and to use it as a talking point against design theorists.

Your argument is wrong in several ways. First, it is an ad hominem. Second, examining an argument is still part of science. Third, creationists in fact do some original research. I suppose that you don't bother to read their reports. If you're going to avoid making such fatuous statements, you will need to educate yourself on the subject matter.

Scott,

Science isn't engineering. I've done research in both. Problem solving in one doesn't translate well to problem solving in the other.

You're still avoiding the point about "junk" DNA having been used as part of the evolutionists' apologetic. Concede the point, say that science makes progress, and move on.

Really. Can you name some of these scientists who have made significant contributions to genetics who don't 'take evolution seriously'? Specifically, the ones who have found (or likely will find) functions for the junk DNA sequences? Want to place bets as to whether they use creation or evolution as an explanatory framework?

As many others have pointed out, you don't understand what 'junk DNA' means in a scientific context. It's just like most creationist's misunderstanding of 'vestigial'. Vestigial doesn't mean 'no function', and neither does 'junk DNA' Junk DNA simply means non-protein-coding. Some of it most likely is truly useless. Some of it may have some sort of function. (just like ostrich wings, while still being vestigial and useless for flight, are used for balance or shading chicks)

TomH, pointing out the dearth of research from creationists most certainly isn't making an ad hominem; it's simply stating a fact.

Care to share some of this 'creationist' research with us?

Let me get this straight: Are you claiming that all junk DNA has a purpose that is yet to be found? Is it not possible that some of the noncoding segments truly are useless left over remnants from past mutations?

Just give it up with the word games already. You said, "Some of it most likely is truly useless"... see you are still making an evolutionary prediction like those that came before you, however, you have tempered it because of known uses for the so-called junk. Look common sense tells you that evolutionists coined the word "junk" for a reason. Get over it.

Jones wasn't really taken to school, he was taken for a ride and those of us who know the reality of what happens to dissidents of the Darwinian metaphysics take him for an incompetent of the highest order.

Based on what we already know of biosemiotics (Abel & Trevor) and genetic entropy (Sanford), Jones, the ACLU, Miller, Forest and the rest of the witch hunters will be looked upon with as much scorn and wonder as we now look on those consensus fanatics of Galileo's day.

The *source* of the research that may be used to support the creationist position is irrelevant. Your fixation on whether the source is creationist or not is ad hominem. I hope that you realize that an argument from inadequate authority is ad hominem.

If your currency matched your rhetoric, then I wouldn't need to provide any references since you would already know them. However, you are asking for references, so I must conclude that your rhetoric overreached your currency.

Clearly, there is some DNA that may be junk, like DNA for fingers in sharks. I say "may" because it is possible that it has another use. (I've written code that has different uses depending on the variables.) I would think that unnecessary DNA might be eliminated to some degree since it consumes energy to duplicate it.

Zachriel: A simple view of evolution is that it will tend to remove unneeded structures over time. But small, slow reproducing organisms can accumulate and sustain more junk. There are countervailing influences.

Blas: Do you have any examples of both?

It's a mathematical result, though consistent with observation. The rate at which non-functional bases are removed from a genome depends on the biological cost of maintaining and duplicating the excess, population size, and generation rate. Bacteria form very large populations (a quadrillion in the typical human gut), and there is a significant selective benefit to rapid reproduction, so bacteria usually have very streamline genomes. In eukaryotes, especially multicellular eukaryotes, the rate of reproduction is slower, the populations smaller, and the selective gradient more slight, so excess bases can accumulate faster than they can be removed.

Derick Childress: "pointing out the dearth of research from creationists most certainly isn't making an ad hominem; it's simply stating a fact.

Care to share some of this 'creationist' research with us?"

Tom H: If your currency matched your rhetoric, then I wouldn't need to provide any references since you would already know them. However, you are asking for references, so I must conclude that your rhetoric overreached your currency.

Zach: "It's a mathematical result, though consistent with observation. The rate at which non-functional bases are removed from a genome depends on the biological cost of maintaining and duplicating the excess, population size, and generation rate. Bacteria form very large populations (a quadrillion in the typical human gut), and there is a significant selective benefit to rapid reproduction, so bacteria usually have very streamline genomes. In eukaryotes, especially multicellular eukaryotes, the rate of reproduction is slower, the populations smaller, and the selective gradient more slight, so excess bases can accumulate faster than they can be removed."

I´m sorry Zach, I still do not understand what are you saying and in the paper cited by Thorton there is no reference to the accumulation of junk DNA.

I´ll try to refrase: Bacteria can get rid of junk DNA because is an advantage for fast replication.Small eucariotes do not because they are slow replicators.Big eucariotes can get rid of junk DNA faster than small ones.Is that what you are saying?

Blas: I´ll try to refrase: Bacteria can get rid of junk DNA because is an advantage for fast replication.

Yes, there is selective advantage, the populations are large, and reproduction is rapid.

Blas: Small eukaryotes do not because they are slow replicators.

Bacteria are much smaller than eukaryotic cells, like fleas to elephants. Consequently, eukaryotes have much smaller populations, reproduce less quickly, so selection can't remove excess dna as efficiently. For comparision, there are about a quadrillion bacteria in the human gut.

Zach:"Bacteria are much smaller than eukaryotic cells, like fleas to elephants. Consequently, eukaryotes have much smaller populations, reproduce less quickly, so selection can't remove excess dna as efficiently. For comparision, there are about a quadrillion bacteria in the human gut."

But then how do you explain protozoa with almost one thousand more DNA per cell than the average of birds or flatwarms with almost ten times of the average of mammals?

If there isn't then please get to work trying to find positive evidence for your position.

Joe,

You're asking for the impossible, as no observations provide positive observations for any theory, including gravitational theory.

Again, you're acting as if this is unique to evolutionary theory, but it's not. Either your ignorant about how science works or this represents disingenuous hand-waving on your part.

While observations and testable theories are important, the key thing we look for in scientific theories is a chain of hard to vary explanations. Note, this is not merely my opinion. Should you actually look back at historical discoveries, you'll find that explanations were indeed the key factor. However, ID is clearly lacks in regards to hard to vary explanations for the concrete biological complexity we observe.

For example, what is ID's explanation for why 98% of all species that were supposedly designed went extinct? ID simply has no answer. At best, we hear, "that's just what the designer must have wanted", etc.

This lack of explanation regarding the specific biological complexity, rather than a particular class of biological complexity, is why my position does not expand to contain a designer. Again, I don't think we can identify design in biology without knowing anything about the designer.

Specifically, an abstract designer could have designed everything to look unfamiliar to us and nature can form things that appear familiar to what we consider design. Again, this just isn't my opinion, we've seen examples of this time again time again.

Blas: But then how do you explain protozoa with almost one thousand more DNA per cell than the average of birds or flatwarms with almost ten times of the average of mammals?

Not everything is known, but let's consider what we do know. Genome size in eukaryotes is not well-correlated with complexity, and material can be added to genomes through a variety of processes, including genome duplication. Genome size is only somewhat deleterious within limits, and is removed slowly in eukaryotes. Some lineages accumulate dna much faster than others, while higher metabolism organisms, such saurischians and their avian descendants, tend to have more compact genomes, possibly because of increased selection for efficiency.

There are still a lot of questions, but no indication that this is due to anything other than natural mechanisms.

The observation in question did not falsify Einstein's theory of general relativity. This is not the same as providing positive support.

For example, it's logically possible that an army of slide rule toting demons are pushing and pulling on objects in exactly the same way as if space-time was curved.

We reject this theory because if fails to explain why an army of demons would choose to exert forces in a consistent manner, which just so happens to match the same observations predicted if space time is curved.

So, it would seem that you're the one who doesn't know what your talking about.

Zach: “but no indication that this is due to anything other than natural mechanisms.”

Nobody is looking for supernatural mechanisms

Zach: “ Genome size in eukaryotes is not well-correlated with complexity, and material can be added to genomes through a variety of processes, including genome duplication. Genome size is only somewhat deleterious within limits, and is removed slowly in eukaryotes. Some lineages accumulate dna much faster than others, while higher metabolism organisms, such saurischians and their avian descendants, tend to have more compact genomes”

I agree with this observation but then your statement “A simple view of evolution is that it will tend to remove unneeded structures over time.”

is not accurate at least with the DNA of such structures.

Zach: “possibly because of increased selection for efficiency.”

This is only wishfull thinking. I wonder how the protozoa with a genoma thousand times bigger than the average of protozoa genoma was selected against his ancestor with a smaller genoma. Adding junk to the genoma make the protozoa more fittinng? As you say:

Zachriel: A simple view of evolution is that it will tend to remove unneeded structures over time.

Blas: is not accurate at least with the DNA of such structures.

That's why we referred to it as a "simple view."

There is a biological cost associated with excess genomic baggage, hence there is a negative selection bias. That doesn't mean it will be efficiently removed. That depends on the size of the coefficient, the size of the population and the generation time.

Blas: I wonder how the protozoa with a genoma thousand times bigger than the average of protozoa genoma was selected against his ancestor with a smaller genoma. Adding junk to the genoma make the protozoa more fittinng?

That's why we referred to it as a "simple view."

Not every trait is due to selection. Selection is not all-powerful. Drift is often more important in small populations, and removal of excess dna through selection may be slower than the process by which it is added.

Blas: How evolutionist can call their theory a fact?

It's a fallacy to say that because not everything is known that nothing is known. Even if the size of genomes were a complete mystery, that doesn't trump the bulk of evidence supporting the Theory of Evolution.

How would polyploidy be relevant in regards to a mechanism for evolution (perhaps of a hypothetical human-chimp ancestor to a human)? Surely you saw this coming.

Blas,

"Evolution is a fact and a theory." This statement is based on equivocation of meanings for "evolution." It's worth considering the various meanings for "evolution" if we are to improve our communication and reduce the confusing polemics. "Evolution" can mean "changes in gene pool over time" or "changes in the frequency of a gene over time" or "changes in the exclusivity of mating habits of some organisms possibly grouped by geographical distribution and appearance attributes (morphology, color, etc.) or "common ancestry." "Common ancestry," of course, includes a very wide range of possible maps. Neo-darwinian evolution may be meant, or evo-devo, or cooperative evolution, or others meanings. Sometimes abiogenesis and cosmogony are included as well. So, when talking about "evolution," it's important to specify exactly what is meant. I've had pinheads (a technical term for idiots) tell me that I don't know what evolution is when they don't even know that support for the Modern Synthesis is weak among evolutionary biologists.

We've observed new species come into being, where "species" is defined as a group of organisms which has changed its mating selectivity from a parent group to its own new group. Therefore, evolution is a fact. Obviously, common ancestry has far less support than the formation of a new species, so one has to be tentative regarding it. Common Ancestry is a theory, regardless of how much support it has or how tentative we need to be regarding it. Somewhat analogously to common ancestry, gravity is a theory and a fact. The theory (explanation) may be tentative while the evidence for the existence of some unseen material/energy/force may have enough support to call it a fact.

Glad to read this sentence. I agree, and I think this theory has a number of planet epicycle to allow tomove to others explanatory frameworks, unfortunatly for science to much teological prejudice (like yours thinking I were looking for supernatural explanations) prevent it.

TomH: How would polyploidy be relevant in regards to a mechanism for evolution (perhaps of a hypothetical human-chimp ancestor to a human)?

Polyploidy was introduced to address a question about the varying sizes of genomes in eukaryotes, and their apparent unrelation to their selective advantage, the C-value enigma, and how this supposedly this represents an argument against evolutionary theory. As discussed above, this is a misunderstanding of evolutionary theory. We don't expect all traits to have selective value, and there are valid explanations for such wide variation in genome size in eukaryotic species.

(However, the C-value enigma is inconsistent with versions of so-called Intelligent Design.)

TomH: "Evolution is a fact and a theory." This statement is based on equivocation of meanings for "evolution."

TomH"Somewhat analogously to common ancestry, gravity is a theory and a fact. The theory (explanation) may be tentative while the evidence for the existence of some unseen material/energy/force may have enough support to call it a fact."

Gravity is a theory, an explanatory framework. Facts are that the apple fall from the tree, the moon moves around earth, facts are something you can reproduce in your lab or two independant observers can see. In fact, we see stars in the autside of the galaxies that according the estimated masses and speeds needs to "create" the dark matter and the dark energy to fit in the gravity theory.

The statement wasn't ascribed to you, but merely appended. In addition, it was referring to the lack of evidence of artifice, and not a reference to the supernatural.

Blas: Facts are that the apple fall from the tree, the moon moves around earth, facts are something you can reproduce in your lab or two independant observers can see.

Observations are typically considered facts. Facts are also claims that have been well-established. So that the Earth moves was considered a fact long before we could directly observe its movement from space.

Cornelius G. Hunter is a graduate of the University of Illinois where
he earned a Ph.D. in Biophysics and Computational Biology. He is
Adjunct Professor at Biola University and author of the award-winning Darwin’s God: Evolution and the Problem of Evil. Hunter’s other books include Darwin’s Proof, and his newest book Science’s Blind Spot
(Baker/Brazos Press). Dr. Hunter's interest in the theory of evolution
involves the historical and theological, as well as scientific, aspects
of the theory. His website is http://www.darwins-god.blogspot.com/